2022 Environmental Microbiology

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Academic unit or major
Graduate major in Life Science and Technology
Wachi Masaaki  Hongoh Yuichi  Yatsunami Rie  Mcglynn Shawn 
Class Format
Lecture    (Livestream)
Media-enhanced courses
Day/Period(Room No.)
Tue1-2()  Fri1-2()  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
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Course description and aims

On Earth, diverse environments respectively accommodate unique microbiota, and the microbial communities greatly contribute to the global material and energy cycle. In this class, the physiology, ecology, and phylogenetic diversity of environmental microbes, as well as how to investigate them, are outlined, and the applications of environmental microbes are also explained. Prof. Wachi presents the methods of isolation and identification of soil microbes and their applications in agriculture, bioremediation and screening of antibiotics. Prof. Yatsunami explains the ecology of extremophiles and the structures and functions of their enzymes. Prof. Hongoh outlines metagenomics and single-cell genomics of uncultured microbes. Prof. McGlynn explains diverse energy conserving strategies of environmental microbes and outlines arguments on the Last universal common ancestor of extant organisms.

Student learning outcomes

By the end of this course, students will understand and be able to explain the outline of:
1. The phylogenetic diversity, physiology, and ecology of microbes in diverse environments
2. The application of soil microbes in agriculture, bioremediation, and mass production
3. The functions and application of extremophiles


soil microbes, extremophiles, applied microbiology, uncultured microbes, metagenomics, energy conservation, origins of life

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

The lectures are given in English by using PowerPoint slides (ZOOM), which will be uploaded prior to each lecture.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Isolation (cultivation) and identification of soil microbes Understand how to isolate and identify soil microbes
Class 2 Screening of antibiotics from environmental microbes Understand how to isolate microbes producing antibiotics
Class 3 Application of microorganisms in industry Understand the outline of applied microbiology, especially microbial fermentation
Class 4 Introduction; Thermophiles, alkaliphiles, halophiles and their enzymes Explain the thermotolerant, alkalitolerant and halotolerant mechanisms of thermophiles, alkaliphiles, halophiles and their enzymes
Class 5 Piezophiles and their enzymes Explain the piezophilic mechanism of piezophiles and their enzymes
Class 6 Organic solvent–tolerant microbes and their application Explain the organic-solvent-tolerant mechanisms of organic-solvent-tolerant
Class 7 Application of extremophiles and their enzyme in industry Explain the application of extremophiles and their enzyme in industry
Class 8 "Species" in bacteria and microbial community structure analysis Understand a hypothetical definition of "species" in bacteria and how to analyze microbial community structures
Class 9 FISH and metagenomics Understand the outlines of fluorescence in situ hybridization and metagenomics
Class 10 Single-cell genomics and functional genome analysis Understand the outline of single-cell genomics and functional genomics
Class 11 Phenotypic heterogeneity Understand that isogenic populations are not homogeneous in activity, and be able to suggest some possible reasons why
Class 12 Energy conserving strategies Understand the diversity of conservation strategies used in biology, and be able to suggest some that may yet be discovered in the future
Class 13 What is the low energy limit for life? From the previous lecture, construct theoretical arguments of what might be the low energy limit of life on Earth, and compare this with observation
Class 14 How old is biology, and what do we know about the earliest life? Understand uncertainties with the Last universal common ancestor (LUCA); its potential phenotype and its timing

Out-of-Class Study Time (Preparation and Review)

To enhance effective learning, students are encouraged to spend approximately 100 minutes preparing for class and another 100 minutes reviewing class content afterwards (including assignments) for each class.
They should do so by referring to textbooks and other course material.


None required.

Reference books, course materials, etc.

Brock Biology of Microorganisms (14th edition)
Handouts will be distributed at the beginning of class when necessary and elaborated on using PowerPoint slides.

Assessment criteria and methods

Reports or online exams by each instructor.

If your reports are found to contain materials plagiarized from literature, including the Internet, or reports by other students, your grade will be marked zero, and the University may take further disciplinary action.

Related courses

  • LST.A345 : Microbiology
  • LST.A347 : Evolutionary Biology

Prerequisites (i.e., required knowledge, skills, courses, etc.)

No prerequisites are necessary.

Contact information (e-mail and phone)    Notice : Please replace from "[at]" to "@"(half-width character).

Masaaki Wachi (mwachi[at]bio.titech.ac.jp), Yuichi Hongoh (yhongo[at]bio.titech.ac.jp), Rie Yatsunami (yatsunami.r.aa[at]m.titech.ac.jp)、Sahwn McGlynn (mcglynn[at]elsi.jp)

Office hours

Students may approach the instructors through e-mail.

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